The goal of Zea mays L. (corn) breeding is to combine various desirable traits in a single variety/hybrid. Such desirable traits include greater yield, better stalks, better roots, resistance to pesticides, pests and disease, tolerance to heat and drought, reduced time to crop maturity, better agronomic quality, higher nutritional value, and uniformity in germination times, stand establishment, growth rate, maturity and fruit size.
Modern molecular biology and transgenic technologies (genetic engineering) have greatly accelerated the introduction of new genes and, hence, new traits into corn lines. While useful, genetic engineering is hampered by transgene silencing problems. Transgene silencing is a little understood process by which genes introduced by genetic engineering are silenced or turned off. As such, transgene silencing is a major impediment to the use of genetic engineering for corn improvement. At present, the solution to transgene silencing is to search through a large number of transgenic events for transgene loci that are active and stable. This is a painstaking and laborious process, which greatly increases the cost of corn breeding using genetic engineering techniques.
In addition to transgene silencing, there are other examples of gene silencing that are variable, unstable, but heritable. In corn these include the cycling of transposable elements between active and inactive states and paramutation, gene silencing that occurs through interactions between specific alleles of a gene. The mechanism of silencing is not understood in any case, but current hypotheses invoke heritable alterations to chromatin structure.
Although mutants are known in corn that can prevent or reverse gene silencing (U.S. Pat. No. 7,264,970), the molecular identity of these factors remains unknown. There thus remains a need to identify the molecular identity of these factors. There is also a need to reduce or mitigate gene silencing in transgenic plants and to reduce inbreeding depression during plant breeding.